Instream Flow in the Deschutes Basin: Monitoring, Status and Restoration Needs. DWA Final Report

Transcription

1 Instream Flow in the Deschutes Basin: Monitoring, Status and Restoration Needs DWA Final Report August 2006 Brett Golden. 1 Bruce Aylward, Ph.D. 1 1, Deschutes River Conservancy, 700 NW Hill Street, Bend, Oregon 97701, (541)

2 The authors wish to thank the Bureau of Reclamation for sponsoring this report as part of the Deschutes Water Alliance Water 2025 Grant (see for more information).

3 Deschutes Water Alliance Instream Flows in the Deschutes Basin: Monitoring, Status, and Restoration Needs August 2006 Prepared by: Brett Golden Bruce Aylward Deschutes River Conservancy Deschutes River Conservancy Feedback and comments were received from: Patrick Griffiths City of Bend Tod Heisler Deschutes River Conservancy Kate Fitzpatrick Deschutes River Conservancy Steve Johnson Central Oregon Irrigation District & Deschutes Basin Board of Control Jan Lee Swalley Irrigation District John Eustis Crooked River Watershed Council Lesley Jones Upper Deschutes Watershed Council Bonnie Lamb Oregon Department of Environmental Quality Jan Houck Oregon Parks & Recreation Department Steven Marx Oregon Department of Fish and Wildlife Kyle Gorman Oregon Water Resources Department Ken Lite Oregon Water Resources Department Jonathan La Marche Oregon Water Resourced Department Marshall Gannett United States Geological Survey Michelle McSwain Bureau of Land Management April James Oregon State University Gail Achterman Oregon State University

4 FOREWORD BACKGROUND The upper Deschutes Basin comprises about 4,500 square miles of watershed between the highland areas to the east, south and west, and Lake Billy Chinook to the north. The Central Oregon area, located within the upper basin, is experiencing rapid growth and changes in both lifestyle and land uses. Along with these changes, long-recognized water resources issues have become more important and a number of others have developed. More effective use of water resources to broaden the benefits of water use in connection with irrigation, stream flow restoration, protection of scenic waterway flows and water quality improvements has long been an important resource management issue in the upper basin. Other developing issues include need for safe, reliable water supply for future basin needs, urbanization of irrigated lands and impacts on agriculture, and needs to protect flows for fishery, recreation and other instream uses. The significance of basin water issues has increased considerably over the last few years. The rapid growth and subsequent water needs that the region is experiencing presents an opportunity to study these issues in more detail given changing values and availability of funding. Consequently, water usage and availability are now a major topic in discussions among basin water suppliers and planners. Due to increased dialogue and awareness relative to water issues, regional urban water suppliers, irrigation districts and other private, government and individual water users now recognize their interdependency in the use, management and protection of Deschutes Basin water resources. This recognition and related dialogue enjoined the major water suppliers in a common vision that commits energy and resources in a collaborative effort to respond to basin water issues. Water supply, water quality, flow depletion and irrigation district urbanization issues in the upper Deschutes Basin establish the framework for need for the Deschutes Water Alliance. Mutually beneficial opportunities exist for municipalities and flow restoration interests to obtain needed water supply and for irrigation districts to resolve urbanization and conservation issues. Some of the key management considerations involved with these opportunities: Full appropriation of surface waters Declaration of groundwater restrictions and related mitigation requirements Dependency of municipal water providers on groundwater for future needs Diversion of substantial river flows by irrigation districts 303(d) listings for water quality parameters and need for TMDLs throughout the Deschutes and Crooked Subbasins. Protection of scenic waterway flows in the lower reaches of the Deschutes and Crooked Rivers DWA Instream Flows in the Deschutes Basin FW-1

5 Potential Endangered Species Act issues Re-Introduction of anadramous fish species in the Deschutes and Crooked Rivers Rapid growth, urbanization and land-use change in the basin Organization The Deschutes Water Alliance (DWA) was formed by four major basin partners to develop and implement integrated water resources management programs in the upper Deschutes Basin. The partners include: Deschutes Basin Board of Control (DBBC): represents seven irrigation districts in the basin including BOR s Deschutes Project (North Unit Irrigation District) and Ochoco Projects formed under ORS Central Oregon Cities Organization (COCO): which is comprised of cities in the basin and affiliated drinking water districts and private companies providing potable water supply. Deschutes River Conservancy (DRC): Confederated Tribes of Warm Springs (CTWS) Goals and objectives The DWA is investing in managing the water resources of the Deschutes Basin in a unified way to provide: Reliable and safe water supply for the region s future municipal and agriculture needs and sustained economic viability considering growth, urbanization and related effects on water resources; Financial stability for the Basin s irrigation districts and their patrons; Protection of the fishery, wildlife, existing water rights, recreational and aesthetic values of the Deschutes River along with stream flow and water quality improvements; Focus on maintaining the resource and land base in the Basin, consistent with acknowledged comprehensive land use plans; and An institutional framework that supports the orderly development of local water markets to protect participants and create an even playing field for water transactions. These considerations are key elements to be incorporated into development of the integrated water resources management and restoration program. Approach Mutually beneficial opportunities exist to boost water supply for agriculture, municipal needs and stream flow for fish, wildlife and water quality improvements. Mutually beneficial DWA Instream Flows in the Deschutes Basin FW-2

6 opportunities also exist through integrated planning for irrigation districts to resolve urbanization issues. In order to develop a framework and program to achieve these objectives, the DWA is implementing five planning studies under a Water 2025 Program grant to generate facts and background information necessary for program formulation. The planning study results will be synthesized into a Water Supply, Demand and Water Reallocation document with project scenarios, five-year implementation bench marks and 20-year timeframe. The five planning studies are as follows: Irrigation District Water Conservation Cost Analysis and Prioritization-an evaluation and prioritization of opportunities to save water through piping and lining of canals, laterals and ditches, as well as through on-farm conservation technologies. Growth, Urbanization and Land Use Change: Impacts on Agriculture and Irrigation Districts in Central Oregon. (Title in Water 2025 Grant was Impacts of Urbanization on Irrigable Lands) -an inventory of amounts, patterns and rates of district water rights becoming surplus due to urbanization or other changes in land use patterns in Central Oregon and corresponding impact on district assessments. Reservoir Management (Title in Water 2025 Grant was Reservoir Optimization Study and Water Quality)- prepare rapid assessment of potential gains from optimization of existing reservoirs and their potential impact on improving flow and quality, and prepare terms of reference for more formal and rigorous assessment. Future Groundwater Demand in the Deschutes Basin (Title in Water 2025 Grant was Municipal Water Demand)-assessment of the water supply needs, quantity and timeline of the Basin s regional urban suppliers. Instream Flow in the Deschutes Basin: Monitoring, Status and Restoration Needs (Title in Water 2025 Grant was Measurement, Monitoring and Evaluations Systems)- In-stream Flow Needs for Fish, Wildlife and recreation along with Measurement, Monitoring and Evaluation Systems-assessment of the suitability and completeness of existing flow measurement sites and existing Water Quality and Monitoring Plan for the Upper Deschutes Basin and prepare funding and implementation action plan. DWA Instream Flows in the Deschutes Basin FW-3

7 EXECUTIVE SUMMARY The Deschutes Water Alliance working mission includes the objective of moving stream flow toward a more natural hydrograph while securing and maintaining improved instream flows and water quality to support fish and wildlife. The purpose of this paper is to quantify instream flow needs in the upper Deschutes Basin, particularly in those reaches affected by irrigation district water storage and diversion.. The methodology employed to this end is to identify the affected reaches, gather existing data and information on instream conditions and instream flow targets, identify existing senior instream rights and then develop quantitative estimates of stream flow needed to meet flow targets. This information will be used alongside other information on the demands for and the sources of water to develop scenarios for meeting instream, agricultural and community needs over a 20-year time frame. This paper also considers the monitoring and measurement needs required to verify flow and water quality outcomes related to instream flow restoration. Water Resources The paper begins by using existing data to characterize the availability and use of water resources in the upper portion of the Deschutes Basin. Precipitation and lateral movement of groundwater into the basin provide the water resources input available for human and ecosystem use in the upper Deschutes Basin. This input then (a) either evaporates or transpires from the surface or soil moisture (evapotranspiration), largely due to plant growth, (b) percolates through the ground and recharges the aquifer, where it ultimately discharges to surface waters or (c) runs off to surface waters. Ecosystem uses consist of water used to support upland vegetation and ecological processes as well as instream and riparian uses where the hydrograph supports a wide range of physical, chemical, biological and ecological functions of rivers. Human uses occur either directly through capture, diversion or withdrawal of surface and ground waters or indirectly through the harvesting of plants and animals that consume water to grow and reproduce. The assessment focuses on the Groundwater Study Area which comprises the upper Deschutes Basin except for that portion of the Crooked River system above Prineville and Ochoco Reservoirs. Extensive work by the US Geological Survey, estimates of exempt well water use from OWRD, and calculation of irrigation crop water use conducted for this paper suggest that for the Groundwater Study Area human activities over the last 150 years or so have: Stored and diverted a large portion of stream flow, altering stream hydrographs and decreasing summer and winter stream flows in specific places and reaches by 96% to 100% Rerouted surface water flows to increase groundwater recharge by approximately 12%, through transmission and on-farm losses from irrigated agriculture Led to increased consumption (evapotranspiration) on the order of 350,000 acre-feet of water per year (480 cfs) which is equivalent to about 10% of mean annual stream discharge DWA Instream Flows in the Deschutes Basin ES-1

8 Led to the consumption of roughly just over 1% of the annual groundwater flux via groundwater pumping. In sum, human activities have altered the water resource regime in the upper Deschutes Basin to varying degrees. Groundwater consumption comprises a relatively small amount of the annual groundwater flux. Seepage losses from irrigation returning to the regional aquifer are 15 times as large as groundwater withdrawals. The prospect of large-scale implementation of water efficiency projects and increasing groundwater use will affect this ratio going forward and have raised concerns about future seasonal impacts on the lower Deschutes River, the reach where all the changes in storage, diversion and surface-groundwater interactions come together in one place. Overall consumption of annual stream discharge from the Groundwater Study Area is approximately 10%. However dramatic seasonal modifications to the water resources regime in the upper basin are apparent. These are demonstrated by low stream flows in reaches observed below irrigation district diversions and storage facilities. The assessment that the portion of the upper Basin represented by the Groundwater Study Area has only tapped its water resources in a modest manner does not eliminate the need to carefully plan for and regulate the impacts of future changes in water management, particularly as the upper basin sees dramatic changes in land use and types of demand for use of water resources. With instream flow protection and restoration yielding services that are important components of not just the environment in Central Oregon, but the economy, the impacts on stream flow need to be carefully evaluated. Reach Assessment Instream flows are critical to the maintenance of floodplain, riparian, and aquatic ecosystems. Seven of the eight reaches included in the assessment of reach conditions and trends experience water quality or quantity impairments due to flow alteration. In these reaches, flow is highly modified by storage or diversion by irrigation districts. Six of these are in the upper Deschutes Basin, including: Little Deschutes River upper Deschutes River middle Deschutes River Tumalo Creek Whychus Creek lower Crooked River The lower Deschutes River is also included in this assessment, as it is the reach where all water flow changes in the upper Deschutes Basin come together. The Metolius River is included as a reference river that has been largely unaltered by human use. Monitoring, Instream Flows, and Water Quality Water quantity and quality monitoring in each reach allows for an understanding of current status and historic trends. The Deschutes Basin has a relatively comprehensive water quantity DWA Instream Flows in the Deschutes Basin ES-2

9 monitoring system. Each reach discussed in this paper contains two or more gages operated by state or federal agencies. The Oregon Water Resources Department, the United States Geological Survey, and the Bureau of Reclamation publish both historical and near-real time data for these gages, allowing the analysis of both historic trends and current status. Water quality monitoring stations exist on each of the reaches as well. First, the Oregon Department of Environmental Quality s ambient water quality monitoring network provides long term water quality monitoring in several of the reaches discussed in the study. Second, the Upper Deschutes Watershed Council s (UDWC) Water Quality Monitoring Program is a comprehensive, cross-jurisdictional, hydrologic unit based monitoring effort that encompasses six out of the eight reaches discussed here. The UDWC runs the program in coordination with local, state, and federal agencies. Water quality monitoring in the other two reaches, the lower Deschutes River reach and the lower Crooked River reach, is managed by other organizations. Flow alteration has affected instream flow patterns and water quality in seven out of the eight reaches discussed in this study. This study used Oregon s (d) list of impaired waters to identify water quality issues in the Deschutes Basin. The state lists seven of the reaches for not meeting water quality standards for one or more parameters. Temperature, dissolved oxygen, and ph dominate the list of impairments in these reaches, and instream flow reduction contributes to or causes these impairments. The state has not monitored all reaches in the basin and has not monitored for all parameters in each reach, so actual impairments in these reaches and their tributaries may be more extensive than those listed. Fisheries and water quality restoration drive instream flow restoration in the Basin. The reaches historically supported large salmon and trout populations, and several of them still support Endangered Species Act listed salmon and trout. Anadromous salmon re-introduction in three reaches, one reach and two tributaries to other reaches, has drawn attention to water quantity issues in the basin. 303(d) listing has drawn attention to water quality impairments. ODFW has applied for and received instream water rights to support aquatic life in most reaches of the Deschutes Basin. This study used the instream water rights applied for by ODFW as preliminary flow targets. The targets were set as minimum flows to support salmon and trout populations. Whether they are sufficient to meet state and federal water quality standards and restore aquatic and riparian ecosystem function is not assured. Current research suggests that ecosystem processes depend on the volume and timing of stream discharges. Both high flow and low flow events are important in supporting these processes. Further scientific work to assess ecosystem needs for water may be helpful in order to better assess the likelihood of success of ongoing and future restoration efforts. Reservoir storage and releases for irrigation have highly altered flows in five of the seven water quality impaired reaches in the basin. The upper Deschutes River reach does not often meet target flows in the winter due to upstream reservoir storage. Irrigation diversions have reduced summer flows in six of the seven water quality impaired reaches. Most reaches experience low summer flows due to irrigation diversions, and some reaches experience low winter flows due to irrigation water storage (see Table ES-1). Prior to current restoration efforts, sections of Whychus Creek and Tumalo Creek typically dried up during the irrigation season due to DWA Instream Flows in the Deschutes Basin ES-3

10 extensive diversion. The daily probability of reaching flow targets during each month appears below. Table ES-1. Probability of meeting instream flow targets under managed conditions Month Little Deschutes River Upper Deschutes River Probability of Meeting Instream Flow Target in Selected Reaches* Middle Deschutes River Tumalo Creek Whychus Creek Lower Crooked River Metolius River Lower Deschutes River Jan Low Low Very High Very High Very High Very High Very High High Feb Low Low Very High Very High Very High Very High Very High High Mar Low Low Very High Low Very High High Very High Very High Apr Medium High Medium Low Low High Very High High May Medium Very High Very Low Low Medium Low Very High High Jun Medium Very High Very Low High Medium Low Very High High Jul Very High Very High Very Low Low Very Low Medium Very High High Aug Very High Very High Very Low Very Low Very Low High Very High Very High Sep High Very High Very Low Very Low Very Low Very High Very High Very High Oct Very Low High Medium Medium Very Low Very High Very High Very High Nov Very Low Very Low Very High Very High Very High Very High Very High Very High Dec Low Low Very High Very High Very High Very High Very High Very High *period of record varies for each reach Key to Table ES-1 Percent of Days Meeting Target Probability % Very High 60-79% High 40-59% Medium 20-39% Low 0-19% Very Low Federal and state regulatory approaches all have the potential to affect instream flow allocation in the Deschutes Basin. Federal approaches include the Wild and Scenic Rivers Act, the Clean Water Act, and the Endangered Species Act. State approaches include the State Scenic Waterways Act and instream flow rights to support aquatic life. Voluntary, market-based approaches, enabled by the state legal framework, provide the greatest opportunity for restoring instream flows in the Deschutes Basin. Tools available include instream transfers, leases, storage leases, allocation of conserved water. The Deschutes River Conservancy, local irrigation districts and state and federal partners are working together to restore water to reaches by using these tools. The Deschutes Water Alliance (see foreword) intends to meet instream, agricultural and community needs for water resources. For the purposes of development of long-range planning scenarios for water management in the upper Deschutes Basin, the findings of this paper can be used as preliminary assessment of instream flow demands in the most altered reaches (see ES-2). Scenarios for meeting these needs and those developed in the other DWA papers may then be subjected to further analysis to assess the nature of their impact on the lower Deschutes, with the DWA Instream Flows in the Deschutes Basin ES-4

11 expectation that flows in this reach may also be improved under the scenarios for restoring flows in upper basin reaches. Table ES-2. Summary of instream flow needs for DWA priority reaches Reach Storage Release Requirements (AF) Conversion of Summer Irrigation Water Rights (cfs) Upper Deschutes River 62,500 Middle Deschutes River Tumalo Creek 14 Wychus Creek 14 Lower Crooked River 18,000 The total volume of water represented by these instream needs is just over 183,000 acre-feet. Over the course of a 214-day irrigation season, this volume is equivalent to a rate of 430 cfs. To put it in a larger context, it is 2% of total available water resources and 5% of unregulated blue water flow for the Groundwater Study Area portion of the upper Deschutes Basin. Despite the relatively minor portion of overall water this need represents, the technical, operational and financial challenge will be significant. At approximate current average costs for large conservation projects and instream transfers of $600/acre-foot the total price tag for projects would reach $110 million. However, it is likely this cost will rise as more costly conservation projects are brought on line. Social coordination in terms of the collaboration between a wide range of groups and individuals in the basin will also require a major effort and implies additional costs. DWA Instream Flows in the Deschutes Basin ES-5

12 Table of Contents 1. Introduction Federal Legal Framework Wild and Scenic Rivers Act Endangered Species Act Clean Water Act State Legal Framework Minimum Perennial Stream flows Oregon Scenic Waterways Instream Water Rights Establishing New Instream Water Rights Establishing Senior Instream Water Rights Deschutes Groundwater Mitigation Program Water Resources Assessment: upper Deschutes River Basin Overview of Basin Hydrology Water Resources Development Methods and Data Results Findings and Conclusions Reach Assessment Study Area Little Deschutes Subbasin Upper Deschutes Subbasin Lower Crooked Subbasin Lower Deschutes Subbasin Monitoring and Measurement Flow Monitoring Water Quality Monitoring Reach Status Little Deschutes subbasin, Little Deschutes River Upper Deschutes watershed; upper Deschutes River Upper Deschutes watershed; middle Deschutes River Tumalo Creek watershed; Tumalo Creek Whychus Creek watershed; Whychus Creek Lower Crooked Subbasin; lower Crooked River Lower Deschutes subbasin; lower Deschutes River Metolius River watershed; Metolius River Reach Status Discussion Conclusions...62 DWA Instream Flows in the Deschutes Basin i

13 References...65 List of Tables Table 1. Federal Wild and Scenic Rivers in the Deschutes Basin... 3 Table 2. State Scenic Waterways in the Deschutes Basin... 6 Table 3. Land area and precipitation Table 4. Major diversions and storage reservoirs in Central Oregon Table 5. Inflows to and Outflows from Lake Billy Chinook Table 6. Consumptive Uses in the Groundwater Study Area Table 7. Time periods used for discharge analysis Table 8. Monitoring activities and parameters Table 9. Water quality stations on the Little Deschutes River Table 10. Water quality monitoring in the upper Deschutes River Table 11. Water quality monitoring in the middle Deschutes River Table 12. Water quality monitoring in Tumalo Creek Table 13. Water quality monitoring in Whychus Creek Table 14. Water quality monitoring in the lower Crooked River Table 15. Water quality monitoring in the lower Deschutes River Table 16. Water quality monitoring in the Metolius River Table (d) listed sections of the Little Deschutes River Table 18. Target attainment in the Little Deschutes River, Table 19. Annual differences in volume between storage season* discharge in the Little Deschutes River and instream flow targets Table (d) listed sections of the upper Deschutes River Table 21. Target attainment in the upper Deschutes River Table 22. Annual differences in volume between daily storage season discharge* in the upper Deschutes River and instream flow targets Table (d) listed sections of the middle Deschutes River Table 24. Target attainment in the middle Deschutes River, Table 25. Differences between historic monthly discharge and instream flow targets in the middle Deschutes River, Table 26. Target attainment in Tumalo Creek, Table 27. Water availability, use and instream flow need in Tumalo Creek Table (d) listed sections of Whychus Creek Table 29. Target attainment in Whychus Creek, Table (d) listed sections of the lower Crooked River Table 31. Target attainment in the lower Crooked River, Table 32. Differences between historic monthly discharge and instream flow targets in the lower Crooked River, water years Table 33. Annual differences in volume between daily discharge in the lower Crooked River and instream flow targets, water years Table (d) listed sections of the lower Deschutes River Table 35. Target attainment in the lower Deschutes River, Table 36. Historic probability of meeting instream flow targets DWA Instream Flows in the Deschutes Basin ii

14 Table 37. Analysis of instream flow needs in selected reaches List of Figures Figure 1. Deschutes Basin Figure 2. Reservoir levels and stream/canal gaging: The Teacup Diagram showing gage readings for February 22, Figure 3. The Blue Whale: Flow Regulation in the Deschutes Figure 4. Instream flows in the Little Deschutes River, Figure 5. Instream flows in the upper Deschutes River, Figure 6. Instream flows in the middle Deschutes River, Figure 7. Instream flows in Tumalo Creek, Figure 8. Instream flows in Whychus Creek, Figure 9. Instream flows in the lower Crooked River, Figure 10. Instream flows in the lower Deschutes River, Figure 11. Instream flows in the Metolius River near Grandview, List of Appendices Appendix A. Certificated instream flow rights in the Deschutes Basin Appendix B. Summary discharge data for selected reaches Appendix C. Water Availability in Whychus Creek: Analysis of Hydrology and Characterization of Water Rights DWA Instream Flows in the Deschutes Basin iii

15 1. Introduction National and international interest in instream flow restoration has increased over the last three decades. A recent study found 207 methods to determine instream flow needs across 44 countries (Tharme 2004), demonstrating widespread interest in instream flow restoration. Motives driving river restoration efforts include ecosystem restoration, habitat restoration, flood control, recreation and aesthetics, floodplain reconnection, sediment management, bank protection, and water quality improvements (Whiting 2002; Wheaton 2005). Instream flow restoration efforts in the Deschutes Basin have followed the global trend and have increased over the last decade. Instream flows are critical to the maintenance of floodplain, riparian, and aquatic ecosystems. A multitude of studies have suggested that instream flows drive ecological processes in these systems (e.g. Baron and Poff 2004; Thoms and others 2004; Poff and others 1997). In particular, Poff and others (1997) highlighted the rate and timing of discharge as critical factors for ecosystem health. Water management affects the rate and timing of discharge and can reduce ecosystem health. Altering flows can reduce floodplain connectivity (Thoms and others 2004), negatively impact aquatic ecosystems (Baron and Poff 2004), and reduce biodiversity (Hauer and Lorang 2004). Periodic or prolonged droughts in a stream, including those caused by water management, can influence stream morphology and affect fish populations (Hakala and Hartman 2004). Flow alterations can also cause water quality impairments such as increased stream temperature. Numerous studies outline the effects of stream flow alteration in the Deschutes Basin on water quality, habitat, and fish and wildlife (e.g. NPCC 2004; SWRB 1961; USDA 1997; USDA 1996a; UDWC 2003; Reclamation 1997; Aney and others 1967; Grant and others 1999). These alterations of the natural hydrograph come from withdrawals that reduce flow rates, reservoir storage that reduces flow rates, reservoir releases that artificially increase flow rates, and increases in groundwater recharge/discharge from irrigated agriculture. In 1961 the State Water Resources Board concluded that while the total basin yield is adequate to supply all existing and contemplated future needs of water... simultaneous use of any major portion of existing rights results in flows at or near the zero level in many streams during the summer months (SWRB 1961). The state of Oregon has listed 1,219 miles of streams in the Deschutes Basin for water quality impairments under Section 303(d) of the Clean Water Act (DEQ 2002). These listings are primarily for temperature, dissolved oxygen, and ph impairments, but also included chlorophylla, turbidity, and sedimentation impairments. Stream dewatering from agricultural diversions has been identified as the most important factor contributing to these water quality impairments (UDWC 2003). The Deschutes Water Alliance working mission includes the objective of moving stream flow toward a more natural hydrograph while securing and maintaining improved instream flows and DWA Instream Flows in the Deschutes Basin 1

16 water quality to support fish and wildlife. The purpose of this paper is to quantify instream flow needs in the upper Deschutes Basin, particularly in those reaches affected by the storage and diversion of water by irrigation districts. The methodology employed is to identify the affected reaches, gather existing data and information on instream conditions and instream flow targets, identify existing senior instream rights and then develop quantitative estimates of stream flow restoration needed to meet flow targets. This information will then be used alongside other demands for water and the sources of supply to develop scenarios for meeting instream, agricultural and community needs over a 20-year time frame. This paper also, therefore, considers the monitoring and measurement needs required to verify flow and water quality outcomes. The paper begins with a summary of the state and federal legal framework as it relates to instream flow protection. An introduction to water resource management at the scale of the upper Deschutes Basin is then provided based on existing data. The impacts of human settlement and a century and a half of water resources development are then briefly assessed in terms of the distribution and consumption of surface water and groundwater in the upper basin. The paper then turns to a reach-by-reach consideration of monitoring and measurement capability for flow and water quality, followed by a review of existing information and studies on the conditions and trends in each reach. The paper highlights water quality impairments, current instream flow status, instream flow targets, and critical periods for flow restoration in each reach. An effort is made at the end of each reach section to identify and quantify the instream flow required to meet stated targets. 2. Federal Legal Framework Federal laws and related programs create a supporting framework for instream flow and water quality protection. Specifically, the Wild and Scenic Rivers Act, the Clean Water Act as amended (CWA), and the Endangered Species Act (ESA) provide regulatory mechanisms for protecting or restoring instream flows and water quality. Each of the following Acts provides a layer of regulatory protection for instream flows. Ultimately, however, instream flows can only be protected from diversion under state law. 2.1 Wild and Scenic Rivers Act The federal Wild and Scenic Rivers Act created a program designed to protect the character of free flowing rivers. Enacted in 1968, the Wild and Scenic Rivers Act created several categories of rivers with different levels of protection for each category. The program is currently administered by the National Park Service. Section 7 of the Wild and Scenic Rivers Act provides minimal protection for instream flows. Section 7 prohibits federal assistance to or the federal licensing of water resource development projects within listed sections of river. Additionally, Section 7 prohibits federal agencies from recommending any activities that will negatively affect the unique characteristics of a listed reach without adequately notifying Congress, the Secretary of Agriculture, and/or the Secretary of the Interior. Individual states administer management programs for each federally listed reach within their boundaries, and the federal government has authorization to acquire land along each DWA Instream Flows in the Deschutes Basin 2

17 reach to maintain the character of the river (16 U.S.C ). However, the Wild and Scenic Rivers Act does not authorize federal regulation of water diversions, nor does it authorize federal acquisition of instream water rights. The Wild and Scenic Rivers System includes ten rivers in the Deschutes Basin. Six of these rivers are considered in detail in this paper (see Table 1). This paper does not considered instream flow issues on four of the Basin s Wild and Scenic Rivers: Crescent Creek, Big Marsh Creek, the White River, or the North Fork of the Crooked River. These rivers clearly provide ecological and social value, but they do not fall within the scope of the paper. Table 1. Federal Wild and Scenic Rivers in the Deschutes Basin Waterway Description Little Deschutes River From its source to the north section line of Section 12, T26S, R7E Middle Deschutes River From Wikiup Dam to the Bend Urban Growth Boundary; From Odin Falls to the upper end of Lake Billy Chinook Whychus Creek Source to USGS Gage Lower Crooked River From the National Grassland boundary to Dry Creek Lower Deschutes River From the Pelton Reregulating Dam to the confluence with the Columbia River Metolius River From the Deschutes National Forest boundary to Lake Billy Chinook Source: National Park Service (No date available) 2.2 Endangered Species Act The Endangered Species Act (ESA) sets the preservation of biodiversity as its highest priority. Under the ESA, NOAA Fisheries or the United States Fish and Wildlife Service (FWS) list species as threatened or endangered. The ESA prohibits both federal actions that jeopardize listed species and private actions that result in the taking 2 of listed species. Court rulings have explicitly identified that habitat modification can lead to a taking even if the modification does not affect a specific individual member of the species (e.g. Babbitt v. Sweet Home 1995). The ESA authorizes for civil and criminal suits to be brought against entities that violate its substantive or procedural provisions (16 U.S.C ). The ESA protects threatened or endangered populations or habitat of listed salmon and trout in the Deschutes Basin. Federal actions in the Klamath Basin have demonstrated the power of the ESA to change water allocation. In 2001, Reclamation released a proposed 2001 Operation Plan for the Klamath Project. Subsequently, NOAA Fisheries and FWS issued opinions that Reclamation s proposed 2001 Operation Plan would harm three listed species. Reclamation approved an alternative plan that protected these species but curtailed water deliveries to the Klamath Irrigation District (KID). KID sued the federal government claiming an illegal taking of their property (Klamath Basin Irrigators v. United States 2005). This case illustrates the difficulties associated with using regulatory approaches to protect instream flows. The Deschutes River and its tributaries provide spawning habitat for several populations of ESA listed fish. Both wild summer steelhead and bull trout are currently listed as threatened under the 2 In this context. take means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct (16 U.S.C. 1532) DWA Instream Flows in the Deschutes Basin 3

18 ESA. Historically, these two species thrived throughout the Basin. However, flow modification and habitat degradation have reduced available spawning habitat and limited population sizes (ODFW 2003). Historically, bull trout were found throughout the Deschutes River, the Little Deschutes River, and the lower Crooked River (NPCC 2004; ODFW 2003). Documented bull trout spawning currently occurs in the Warm Springs River, Shitike Creek, and the Metolius River and its tributaries. Bull trout have been found in lower Whychus Creek, the Crooked River, and the middle Deschutes River, but no documented spawning has occurred in those areas (ODFW 2003). According to ODFW (2003), the bull trout population has been increasing above Lake Billy Chinook since In all likelihood, this increase is due to restrictions on harvest. Spawning distribution has increased as harvest has increased (ODFW 2003). Summer steelhead were historically found throughout the Deschutes Basin. Documented spawning occurred in the Crooked River and its tributaries and the Deschutes River its tributaries below Steelhead Falls (ODFW 2003). The elimination of fish passage at the Pelton Round Butte Project eliminated steelhead from the upper Deschutes Basin. Steelhead currently spawn throughout the lower Deschutes River and its tributaries (NPCC 2004; ODFW 2003). The Pelton Round Butte Project may not limit steelhead populations in the future. As part of a hydropower re-licensing agreement, Portland General Electric and the Confederated Tribes of Warm Springs agreed to restore passage at the project and re-introduce anadromous fish to the upper Deschutes Basin. In particular, they plan to re-introduce steelhead to Whychus Creek and to tributaries of the lower Crooked River. The re-introduction of threatened species to the upper Deschutes Basin has the potential to affect future water allocation. 2.3 Clean Water Act Congress originally intended the Federal Water Pollution Control Act Amendments of 1972, as amended and known as the Clean Water Act (CWA), to achieve the broad goal of restoring and maintaining the chemical, physical, and biological integrity of the nation's waters. In the early implementation of the CWA, efforts focused on addressing discharges from traditional pointsource facilities such as municipal sewage plants and industrial facilities. Implementation of the CWA led to water quality improvements in many of the nation s degraded waterways. The CWA s emphasis over the last decade has evolved from a source-by-source, pollutant-bypollutant approach to a holistic watershed-based approach. To make progress towards the goal, states develop water quality standards based on designated uses and water quality criteria. States monitor waterbodies to determine whether the water quality standards are met, and water bodies that do not meet water quality standards are placed on the state s 303(d) list and reported to the EPA. The EPA requires states to develop Total Maximum Daily Loads (TMDLs) for each pollutant entering a listed waterbody. The TMDLs describe the amount of each pollutant that the waterbody can receive without violating water quality standards. In conjunction with the TMDL s, states develop Water Quality Management Plans that outline management activities DWA Instream Flows in the Deschutes Basin 4

19 which will be undertaken by agencies and landowners to help meet water quality standards in listed water bodies. The CWA specifically does not affect existing water rights or the rights of states to allocate water (33 U.S.C. 1251). As the state develops TMDLs and Water Quality Management Plans, though, agencies or individuals may develop voluntary changes in water management that will help to meet the water quality standards. By highlighting factors limiting stream ecosystem health, the CWA has potential impacts water quality and quantity management in the Basin. 3. State Legal Framework Oregon state laws and programs provide the primary basis for instream flow restoration in the Deschutes Basin. State actions range from early minimum flow regulations to instream water right legislation. The state s framework currently provides for instream water rights that are equivalent in status to consumptive use rights. 3.1 Minimum Perennial Stream Flows The Oregon legislature recognized early on that water is a limiting resource in Oregon. In 1955, the legislature passed a comprehensive multiple purpose water bill which addressed instream flow needs (Bastasch 1998). The Act recognized the value of instream flows to support recreation, aquatic life, and pollution abatement, and it provided for the development and protection of minimum flows to support these activities (Bastasch 1998; OAR ). The priority date of a minimum flow was the date on which the state requested the flow. The state set minimum flows on 547 reaches between 1958 and 1988 by administrative rule. The legislature repealed the state s authority to set additional minimum perennial flows in The 1955 legislation contained three weaknesses. First, minimum flows were junior to senior water rights. Second, minimum flows were based on administrative rules, not on water rights. The state often suspended these rules to meet other objectives. The third weakness in the state s minimum flow standards came from its fish-centric approach to setting minimum flows. This weakness will be discussed further in other sections of this analysis. 3.2 Oregon Scenic Waterways In 1970, Oregon voters passed the initiative that created the Scenic Waterways Act and initiated the Scenic Waterways program. The state lists waterways through this program in order to protect their unique scenic beauty, recreation, fish, wildlife, or scientific features (OAR ). The program lists waterways under six categories. Each category defines different management goals and allows different activities to occur along and adjacent to the river. The Oregon Parks and Recreation Department administers the Scenic Waterways program. Landowners wishing to pursue a new activity within a quarter mile of a Scenic Waterway may need to notify the Parks and Recreation Commission, and the Commission may deny this activity if it impairs the unique qualities of the waterway. DWA Instream Flows in the Deschutes Basin 5

20 Many of the listed waterways unique qualities depend on adequate instream flows (ORS ). The Scenic Waterways program prohibits new activities in a Scenic Waterway area if those activities would impair flow and if that impaired flow would harm the unique qualities of the waterway. Oregon Senate Bill 1033, passed in 1995, added groundwater pumping to these regulated activities. Table 2. State Scenic Waterways in the Deschutes Basin Waterway Description Deschutes River From Little Lava Lake to Crane Prairie Reservoir Deschutes River From the gaging station below Wickiup Dam to General Patch Bridge Deschutes River From Harper Bridge to the COID diversion structure near river mile 17 Deschutes River From Robert Sawyer Park to Tumalo State Park Deschutes River From Deschutes Market Road Bridge to Lake Billy Chinook (excluding the Cline Falls hydroelectric facility near river mile 145 Deschutes River From the Pelton Reregulating Dam to the confluence with the Columbia River (excluding the City of Maupin) Metolius River From Metolius Springs to Candle Creek Source: Oregon Revised Statutes (No date available) 3.3 Instream Water Rights The majority of the Western states have established statutory or judicial methods to protect instream flows. Nine of the eleven states west of the Rockies use statutory methods to protect instream flows, one state relies on a court ruling, and one state has no statutory or judicial method to protect instream flows (Boyd 2003). Oregon was one of the first states to acknowledge that instream uses were beneficial and to create a framework for instream flow protection. In 1987, the state legislature passed the Instream Water Rights Act and created the statutory framework necessary to establish instream water rights. OWRD holds these rights in trust for the public, but they can be purchased, leased, or gifted to the state by anyone (OAR ). The rights are intended to provide public benefits such as fisheries enhancement, pollution abatement or recreation. OWRD regulates instream rights based on a rate, duty, and priority date in the same manner that they regulate traditional water rights. Instream flow rights may not injure other water rights holders, may not cause the enlargement of a water right, and may not exceed the flows necessary to increase public benefits (OAR ) Establishing New Instream Water Rights The majority of instream water rights held by the state of Oregon are junior water rights. These junior rights are not often met during the summer irrigation season. Many of there rights were converted from minimum perennial stream flows and have the same 1955 or later priority dates as their predecessors. Additional junior instream flow rights have been created since Three state agencies can apply for new instream water rights. When the Department of Environmental Quality (DEQ), Department of Fish and Wildlife (ODFW), or Parks and Recreation Department (OPRD) determine that instream flow rights are not adequate to provide DWA Instream Flows in the Deschutes Basin 6

21 the specified public benefits, they can apply to OWRD for additional instream flow rights (ORS ). In general, instream water rights cannot exceed the estimated average natural flow of a stream. Oregon allows exceptions in streams where high-flow events, such as those that would allow for fish passage, would contribute to public benefits (OAR ). ODFW has successfully applied for instream water rights to support fish populations in the Deschutes Basin. They calculated most of the instream flow requirements by using the Oregon Method. This early technique estimates the amount of water needed in a stream to support the spawning, rearing, and migration of salmon or trout based on the physical characteristics of the stream. For example, the Oregon Method assumes that salmon and trout generally require six inches of water to over a riffle and that Chinook require eight inches of water over a riffle (Marx, pers. communication 2005). While the Oregon Method does not account for as many spatial or temporal factors as more in-depth methods such as the Instream Flow Incremental Methodology (IFIM; FISRWG 2001), it does provide a preliminary estimate of ecosystem water needs. When ODFW applies for an instream water right, they request both minimum and optimum flow rates for a given reach. The minimum flow rate would provide the minimum amount of water needed to sustain salmon and trout populations without allowing for harvest. The optimum flow rate would provide the amount of water needed to support populations that are large enough to allow for cultural, recreational, and commercial harvests (Marx, pers. communication 2005). These instream flow rates support fish populations but do not necessarily provide for ecosystem processes. The actual instream water right granted by OWRD depends on OWRD s estimate of average natural flow (EANF); in most instances, instream water rights do not exceed EANF (Marx, pers. comm. 2006) Establishing Senior Instream Water Rights The techniques described above create junior instream water rights. These rights preclude additional consumptive uses and provide water on paper, but they do not necessarily provide additional wet water instream. Protecting wet water instream requires the creation of instream water rights with senior priority dates. Three techniques allow individuals or agencies to create senior instream water rights. First, individuals or organizations can lease an existing water right for instream use. Oregon s administrative framework allows individuals to lease all or part of their water right for instream use during all or part of the year (OAR ). In the Deschutes Basin, the majority of leased water comes from irrigation districts and their customers. Water rights created through instream leases have the same priority date as the original water right. Leasing water instream provides a flexible, low-cost technique for improving instream flows, but it does not permanently protect water instream. Oregon s legal framework allows individuals to permanently transfer existing water rights instream (OAR ). Permanent water transfers allow individuals to transfer water off of their land while improving instream flows in the basin. They are often associated with a change in the character of the land from agriculture to other uses. As with temporary transfers, instream water rights created through permanent transfers have the same priority date as the originating water right that was transferred instream. DWA Instream Flows in the Deschutes Basin 7